Exploiting EST databases for the development and characterization of EST-SSR markers in blueberry (Vaccinium) and their cross-species transferability in Vaccinium spp

Abstract Expressed sequence tags (ESTs) databases are an increasingly valuable resource for developing SSR markers. However, to date, only a limited number of SSR markers have been developed from EST databases for blueberry. In this study, 17,267 ESTs in blueberry ( Vaccinium spp.) were screened for SSRs with motif lengths varying from 2 to 6 base pairs (bp). In total, 2187 SSRs (12.67% of total screened ESTs) were identified from 1876 microsatellite-containing sequences. Dinucleotide repeats follow by trinucleotide repeats were the predominant motif. A total of 54 EST-SSR markers were characterized from 120 primer pairs designed by assaying 12 samples of the Vaccinium genus section Cyanococcus . The primer pairs exhibited a high degree of polymorphism with a mean PIC of 0.772, indicating high level informativeness within these EST-SSRs. The 54 new EST-SSR primer pairs comprising 540 alleles were used to investigate cross-species transferability among 26 accessions, which represented 8 species (three exotic cultivated species and five natural wild species from China) from 6 sections of Vaccinium . The results indicated that cross-species transferability ranged from 68.5% to 88.9%. Cluster analysis and PCoA based on 54 EST-SSR primer pairs were largely consistent with the traditional taxonomy and geographic locations among the materials tested, and both indicated that the EST-SSR primers were effective for the phylogenetic analysis in Vaccinium . Our results showed that those EST-SSR markers displayed considerable polymorphism and high transferability in both cultivated and wild species of Vaccinium , and will contribute to the studies of genetic diversity, linkage mapping, QTL and molecular assisted breeding of Vaccinium crops.